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ORCID16th BCB 2025: Philadelphia, PA, USA
- Xinghua Mindy Shi, Xiaoning Qian, Minghan Chen, Jacob M. Luber, Gail L. Rosen, Yunan Luo:
Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2025, Element Philadelphia Downtown, Philadelphia, PA, USA, October 12-15, 2025. ACM 2025, ISBN 979-8-4007-2200-4
Regular Papers
- Jiarui Li, Zixiang Yin, Zhengming Ding, Samuel J. Landry, Ramgopal R. Mettu:
Rational Multi-Modal Transformers for TCR-pMHC Prediction. 1:1-1:8 - Tsz Pan Tong, Jun Pang:
FlowGRN: Scalable and Dropout-Robust Gene Regulatory Network Inference via Flow Matching-Based Trajectory Reconstruction. 2:1-2:8 - Hyunwoo Yoo, Gail Rosen:
Interpretable Metadata-Based Microbial Risk Prediction Using Large Language Models. 3:1-3:10 - Maxwell Sam, Hailemicael Lulseged Yimer, Salil Desai, Xiaohong Yuan, Jinsheng Xu, Huiming Anna Yu, Letu Qingge:
Addressing COVID-19 Data Imbalance Issue with Multimodal Image Generation. 4:1-4:10 - Xulin Chen, Junzhou Huang:
Fine-Grained Interaction and Task-Driven Fusion of Histology Images and Genomics for Multimodal Cancer Survival Prediction. 5:1-5:10 - Ayca Begum Tascioglu, Flavio Bertini, Laura Pistore, Andrea Fabbri, Danilo Montesi:
Comorbidity Extraction for In-Hospital Mortality Analysis: a Comparison of Regular Expressions and Large Language Models. 6:1-6:10 - Furkan Eris, Ulysse McConnell, Can Firtina, Onur Mutlu:
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques. 7:1-7:10 - Xiaoyang Wang, Christopher C. Yang:
MoE-Health: A Mixture of Experts Framework for Robust Multimodal Healthcare Prediction. 8:1-8:9 - Srinivas Aluru, Anne Benoit, Bora Uçar:
Efficient and effective methods for variant selection. 9:1-9:10 - Monireh Taimouri, Vikram Ravindra:
Predicting Brain Age in Functional Neuroimages using Node Centrality Measures. 10:1-10:9 - Nandini Amit Gadhia, Soumyadip Ghosh, Ritesh Krishna, Anh Nguyen, Michalis Smyrnakis:
An explainable approach to learning feature representations of omics data using optimal transport to improve phenotype stratification. 11:1-11:10 - Bojian Hou, Zhanliang Wang, Zhuoping Zhou, Boning Tong, Zexuan Wang, Jingxuan Bao, Duy Duong-Tran, Qi Long, Li Shen:
Fair CCA for Fair Representation Learning: An ADNI Study. 12:1-12:10 - Yin Liu, Daniel J. Wu, Sarah Bounds, Jiyang Cai:
Identification of Condition-Specific Exosomal miRNA Modules Using a Bayesian Framework. 13:1-13:8 - Zheyi Cai, Yinghui Jiang, Changzhi Jiang, Lian Shen, Hongpeng Qiu, Yuan Lin, Juan Liu, Xiangrong Liu:
ChiralRetro: Chirality-Sensitive Encoding and Enhanced Pathway Strategies in Retrosynthesis. 14:1-14:10 - Alon Luboshitz, Michal Rahimi, Ayal Hendel, Yaron Orenstein:
EpiCRISPR: Improving CRISPR/Cas9 on- and off-target prediction by flanking sequences, epigenetic marks, and high-throughput datasets. 15:1-15:10 - Ravi Chandra Thota, Yusuf Sarwar Uddin, Majid Bani-Yaghoub, Mohamed Nezar Abourraja, Gary Sutkin, Susanna Paschal:
Enhancing Agent-Based Models with Real-Time Movement Data to Assess Impacts of Biosecurity Interventions on Disease Exposure in Healthcare Settings. 16:1-16:10 - Frederick H. Xu, Duy Duong-Tran, Heng Huang, Andrew J. Saykin, Paul M. Thompson, Christos Davatzikos, Yize Zhao, Li Shen:
Characterizing Amyloid Pathogenic Spread in Alzheimer's Disease Through A Network Diffusion Model. 17:1-17:9 - Irsyad Adam, Steven Swee, Erika Yilin Zheng, Ethan Ji, William Speier, Ding Wang, Alex A. T. Bui, Wei Wang, Karol E. Watson, Peipei Ping:
ATHENA: Atherosclerosis through Hierarchical Explainable Neural Network Analysis. 18:1-18:9 - Enshi Zhang, Varun Sai Raigir, Christian Poellabauer, Adrian Kohut, John Michael Templeton, Ananda Mondal, Lexi Weintraub:
MADSurv: An Uncertainty-Aware Framework for Multimodal Cancer Survival Analysis. 19:1-19:8 - Sophie Kearney, Shu Yang, Zixuan Wen, Bojian Hou, Duy Duong-Tran, Tianlong Chen, Jason H. Moore, Marylyn D. Ritchie, Li Shen:
Enabling Few-Shot Alzheimer's Disease Diagnosis on Biomarker Data with Tabular LLMs. 20:1-20:10 - Afsana Ahsan Jeny, Sahand Hamzehei, Mostafa Karami, Stephen Andrew Baker, Tucker Van Rathe, Clifford Yang, Sheida Nabavi:
Longitudinal Tumor Generation in Mammograms via Dual Encoder GAN and Learnable Blending. 21:1-21:10 - Steven Tan, Sina Majidian, Benjamin Thomas Langmead, Mohsen Zakeri:
Movi Color: fast and accurate taxonomic classification with the move structure. 22:1-22:10 - Micky C. Nnamdi, Wenqi Shi, Cheng Wan, J. Ben Tamo, Benjamin M. Smith, Chad Purnell, May Dongmei Wang:
KindSleep: Knowledge-Informed Diagnosis of Obstructive Sleep Apnea from Oximetry. 23:1-23:10 - Yishan Zhong, Wenqi Shi, J. Ben Tamo, Micky C. Nnamdi, Yining Yuan, May Dongmei Wang:
Multi-Agent LLM Reasoning for Clinical Procedure Sequencing from High-Granularity EHR Data. 24:1-24:12 - Atishay Jain, David H. Laidlaw, Ying Ma, Ritambhara Singh:
Improved Spatial Transcriptomics Clustering with Nested Graph Neural Networks. 25:1-25:10 - Md Mozaharul Mottalib, Thao-Ly T. Phan, Rahmatollah Beheshti:
HyMaTE: A Hybrid Mamba and Transformer Model for EHR Representation Learning. 26:1-26:9 - Yining Yuan, J. Ben Tamo, Wenqi Shi, Yishan Zhong, Micky C. Nnamdi, B. Randall Brenn, Steven W. Hwang, May Dongmei Wang:
Developing Fairness-Aware Task Decomposition to Improve Equity in Post-Spinal Fusion Complication Prediction. 27:1-27:10 - Al Shahriar Rubel, Frank Y. Shih, Fadi P. Deek:
MoE-MSC: Mixture of Experts with Multi-Stream Connector for Modality-Aware Medical Image Captioning. 28:1-28:8 - Wei Wang, Po-Yu Liang, Jun Bai:
DeepPH : A Multimodal Deep Learning Model for Predicting Enzyme Optimal pH Range. 29:1-29:10 - Iyanu Oduwole, Mengling He, Ratish Kumar Chandrakant Jha, Adrienne Hoarfrost, Andrew D. Steen, Scott J. Emrich:
Transformer-based Prediction of Microbial Growth Rates from Genomic Data. 30:1-30:9 - Libina Bovan Thomas, Ali Risheh, Negin Forouzesh:
Multi-Objective Loss Function For Free Energy Calculations. 31:1-31:10 - Shiv Shankar, Madalina Fiterau:
Augmenting Randomized Controlled Trials with Foundation Models as Synthetic Units. 32:1-32:8 - Khartik Uppalapati, Bora Yimenicioglu, Adan Eftekhari, Shakeel Abdulkareem:
Rare Disease Phenotyping via Self-Supervised Multimodal Learning. 33:1-33:10
Short Papers
- Zerui Xu, Fang Wu, Yingzhou Lu, Yuanyuan Zhang, Yue Zhao:
Retrieval-Reasoning Large Language Model-based Synthetic Clinical Trial Generation. 34:1-34:6 - Yifan Wang, Ananth Grama, Vikram Ravindra:
Deconvolving Complex Neuronal Networks into Interpretable Task-Specific Connectomes. 35:1-35:6 - Mert Gökpinar, Yasin Almalioglu, Mustafa Taha Koçyigit, Tamer Kahveci, Derya Demir, Kayhan Basak, Mehmet Turan:
Vision transformer supported Kolmogorov-Arnold networks for survival prediction in lung cancer. 36:1-36:6 - Glen Rogers, James R. Brown, Bahrad A. Sokhansanj, Joshua Chang Mell, Gail L. Rosen:
MicroTraitLLM: A RAG-based, Microbe-focused LLM for Researchers. 37:1-37:6 - Eitan Tannenbaum, Dana Markiewitz, Tomer Kalisky, Hillel Kugler:
Characterizing Gene Regulatory Network Ensembles in Kidney Injury and Repair. 38:1-38:6 - Faith Abiria Ocitti, Charlotte Versavel, Samuel Sledzieski, Lenore Cowen:
RDS: A ReCIPE for Overlapping Community Detection in Biological Networks. 39:1-39:6 - Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow:
Species detection for microbiomes with TIPP-SD. 40:1 - Maryam Ghasemian, Lynette Hammond Gerido, Erman Ayday:
Privacy-Preserving Collaborative Population Stratification with Dynamic Algorithm and Hyperparameter Selection. 41:1-41:6 - Sakshar Chakravarty, Stefano Lonardi:
Towards optimal selection of ultra-deep sequencing reads for de novo genome assembly. 42:1-42:6 - Ahmad F. Al Musawi, Pratip Rana, Sibtanu Raha, Joshua Braunstein, William C. Sleeman, Rishabh Kapoor, Preetam Ghosh:
ICU-Length of Stay Prediction on Electronic Health Records using Graph Neural Networks and Homogeneous Similarity Graphs. 43:1-43:6 - Junqi Long, Jianqiang Li, Guangzhi Qu, Kun Liu, Bo Liu:
CSMSA: Cross-Space Multiscale Adaptive Link Prediction for ceRNA-Mediated Multimolecular Disease Regulatory Networks. 44:1-44:6 - Chang Wang, Ming Zhu, Shengjie Zhai, Buddhadeb Dawn, Shahram Latifi:
Graph-Based Spatio-temporal Attention and Multi-Scale Fusion for Clinically Interpretable, High-Fidelity Fetal ECG Extraction. 45:1-45:6 - Yanteng Zhang, Zibo Zhao, Chuanyi Zhang, Lipei Zhang, Yuxiang Wei, Vince D. Calhoun:
Local Structural Features Analysis of Hemispheres for AD Diagnosis from Brain sMRI. 46:1-46:6 - Vít Skrhák, Hamza Gamouh, David Hoksza:
Hidden in protein sequences: Predicting cryptic binding sites. 47:1-47:6 - Raghav Awasthi, Nishant Singh, Shreya Mishra, Atharva Bhattad, Moises Auron, Charumathi Raghu Subramanian, Ashish Atreja, Kamal Maheshwari, Dwarikanath Mahapatra, Jacek B. Cywinski, Ashish K. Khanna, Francis A. Papay, Piyush Mathur:
GamELY: Human-in-the loop Framework for Scaling Human Evaluation of LLMs in Healthcare. 48:1-48:6 - Praveen Kumar, Vincent T. Metzger, Scott Alexander Malec:
Unsupervised Latent Pattern Analysis for Estimating Type 2 Diabetes Risk in Undiagnosed Populations. 49:1-49:10 - Xulin Chen, Junzhou Huang:
Deconvolution-Enhanced Contrastive Pretraining of Histology Images and Gene Expressions in Spatial Transcriptomics. 50:1-50:6 - Mirza Farhan Bin Tarek, Rahmatollah Beheshti:
Reward Hacking Mitigation using Verifiable Composite Rewards. 51:1-51:6 - Niecia Say, Farhan Tanvir, Moctar Keita, Lilia Chebbah, Muhammad Ifte Khairul Islam, Esra Akbas:
MCL-DMD: Multi-modal Contrastive Learning for Drug-Microbe-Disease Association Prediction. 52:1-52:6 - Thea Traw, Quoc Nguyen, Layla Oesper, Eric Carlson Alexander:
VECTr: Visualizing Distance Measures for Clonal Trees. 53:1-53:6 - Soumeek Mishra, Corey Curran, Tianyan Lin, John S. Erickson, Kristin P. Bennett:
CTSuggest: An LLM-powered Open Source Application to support Clinical Trial Design by Suggesting Baseline Features. 54:1-54:6 - Md Ishtyaq Mahmud, Veena Kochat, Suresh Satpati, Jagan Mohan Reddy Dwarampudi, Kunal Rai, Tania Banerjee:
Benchmarking Dimensionality Reduction Techniques for Spatial Transcriptomics. 55:1-55:6 - Shaun Qien Yeau Tan, Shaunna Wang, Chia-Pei Wang, Alexandru C. Florea, Isabella W. Wang, Degel S. Agoreyo, Joline J. Speck, Micky C. Nnamdi, J. Ben Tamo, Benoit Louis Marteau, Yishan Zhong, Selina Poon, May Dongmei Wang:
A Hybrid Deep Learning Framework for Automated Cobb Angle Estimation in Scoliosis Assessment. 56:1-56:6 - Sakhawat Hossain Saimon, Tanzira Najnin, Jianhua Ruan:
Pan-cancer Outcome Prediction using Multi-classifier Systems. 57:1-57:6 - Tamim Khatib, Shahaddin Gafarov, Justin Strikowski, Mehmet Turan, Tamer Kahveci:
PLATO: Predicting Longitudinally-Aligned Time Observations of biological networks. 58:1-58:6 - Corey Verkouteren, Djalil Sawadogo, Esra Akbas, Mehmet Emin Aktas:
Identifying Top Performing Providers: A Sheaf-theoretic Approach on Healthcare Networks. 59:1-59:6 - Nishant Singh Chouhan, J. Ben Tamo, Oankar R. Patil, Wenqi Shi, Micky C. Nnamdi, Steven Randall Hwang, Kamran W. Shazand, May Dongmei Wang:
From Association to Mechanism: Causal Graph-Based Fine-Mapping of Regulatory SNPs for Functional Validation. 60:1-60:6 - Monica Isgut, Andrew Hornback, Karan Samel, Logan Gloster, Neha Jain, Kyungbeom Kim, May Dongmei Wang:
Interpretable Neural Networks Reveal Gene Interactions Underlying Autoimmune Disease Risk. 61:1-61:6 - Kowshika Sarker, ChengXiang Zhai:
GCVAE: A graph conditional variational autoencoder for feature dependency guided synthetic metabolomic data generation. 62:1-62:6 - Oankar R. Patil, Benoit Louis Marteau, Kamran Shazand, Yuxuan Shen, May Dongmei Wang:
Data-Driven Symbolic Higher-Order Epistasis Discovery with Kolmogorov-Arnold Networks. 63:1-63:6 - Tianxing Zhou, Jialiang Huang, Chenxi Wang, Andreu Paredes-Gallardo, Eryu Xia, Yinghua Zhou, Guangzhong Sun:
TrialPred: an interpretability model based on multimodal data for predicting the duration of clinical trials. 64:1-64:6 - Yongcheng Mu, Jiangwen Sun, Jing He:
Benchmarking and Improving Foundation Model Dietary Estimates from Meal Images. 65:1-65:6
POSTER SESSION: Poster Presentations
- Ewura-Esi Manful, Yasin Uzun:
Identifying master transcriptional regulators with single-cell-based networks. 66:1 - Zainab Ghafoor, Md Shafiqul Islam, Koushik Howlader, Md Rasel Khondokar, Tanusree Bhattacharjee, Sayantan Chakroborty, Adrito Roy, Ushashi Bhattacharjee, Tirtho Roy:
Enhancing Medical AI Safety Through Multi-Agent Evaluation and Iterative Refinement. 67:1 - Fernando Peralta Castro, Jiaqi Zhang, Ritambhara Singh:
Extending Fairness in Single-Cell AI: Evaluating Age, Sex, and Ethnicity Bias with Synthetic Data Augmentation. 68:1 - Jiaqi Zhang, Manav Chakravarthy, Ritambhara Singh:
scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data. 69:1 - Quan Minh Nguyen, Mian Umair Ahsan, Zhanliang Wang, Kai Wang:
PhenoGPT2: A Multimodal Fine-tuned Large Language Models for Phenotype Extraction and Normalization from Clinical Text and Facial Images. 70:1 - Tia Pope, Ahmad Patooghy:
A Million Nectin-1 Permutations Reveal an Order-Driven Feature Landscape. 71:1 - Gauri D. Ket, William Winnett, Arghya Kusum Das:
Distributed Iterative Multi-k-mer Metagenome Assembly with Progressive Graph Simplification and GC-Aware Clustering. 72:1 - Shengtian Huang, Qing Qin, Dawei Liu:
Large-Scale Stance Analysis of Public Discourse on Anti-Obesity Drugs Using Locally Deployed LLMs. 73:1 - Matthieu Vilain, Rasha Mghabghab, Stéphane Aris-Brosou:
Climate Change Drives the Evolution of Influenza A Viruses. 74:1 - Michael Aaron G. Sy, Garrett Ellward, Daniel M. Czyz, Vidhu Kariyawasam, Panayiotis V. Benos, Simone Marini:
Predicting Pneumococcal Meningitis from Demographics and Early AMR Signals. 75:1 - Jessica Schmilovich, Amanda Zint, Anna Katharina Schlusche, Shawn Singh, Margaret Elizabeth Ross, Vanessa Aguiar-Pulido:
Mapping Interneuron Fate Decisions in the Medial Ganglionic Eminence with Single-Cell RNA Sequencing. 76:1 - A. N. M. Nafiz Abeer, Xiaoning Qian, Byung-Jun Yoon:
A Dual Graph Encoder Approach to Structure-Based TCR-pMHC Binding Prediction. 77:1 - Li Sa, Tianle Ma:
Graph Neural Network with Pretrained Embeddings for Cancer and miRNA Regulator Discovery. 78:1 - Marianna Milano, Pietro Hiram Guzzi:
Novel Graph Neural Network Method for Differential Network Analysis in Biological Data. 79:1 - Rithik Vir:
Early Assessment of Parkinson's Disease Using Spatiotemporal Analysis of Ground Reaction Forces From a Wearable Sensor. 80:1 - Praveen Kumar Guttula, Maria Iftesum, Manas Ranjan Gartia:
Bioinformatics-Driven Lipidomics and Network Modeling Reveal Cardiolipin Remodeling as a Regulatory Switch in Osteogenesis. 81:1 - Archarlie Chou, Juan Arroyo, Brett E. Pickett:
Uncovering Disease-Relevant Regulatory Modules in Bulk RNA-Seq via GRN Clustering, Text Mining, and Enrichment: A Case Study in SHS-Induced Preeclampsia. 82:1 - Marmar R. Moussa, Mohamed Abdelnaby:
Predicting T-Cell Receptor Specificity and Phenotype Using Integrated Classical and Pre-Trained Protein Language Models. 83:1 - Haotian Ma, Daifeng Wang:
SegJointGene: Joint Cell Segmentation and Spatially Gene Prioritization by an Iterative Deep Learning Framework. 84:1 - Hansoo Chang, Ashni Kumar, Joshua Suh, Kevin Street, Ana Ferariu, Alexei Taylor, Kunjal Patel, Sean Brummel, Paige Williams, Lei Wang, Fengqing Zhang:
Investigating Pace of Biological Aging as a Mental and Physical Health Biomarker in Youth with Perinatally-Acquired HIV. 85:1 - Shubham Mohole, Hongjun Choi, Shusen Liu, Christine Klymko, Shashank Kushwaha, Derek Shi, Wesam A. Sakla, Sainyam Galhotra, Ruben Glatt:
VERIRAG: Healthcare Claim Verification via Statistical Audit in Retrieval-Augmented Generation. 86:1 - Enos Dk Kakwambi, Tuan Nguyen, Suryaveer Kapoor, Marmar R. Moussa:
A novel approach to highly variable genes selection for scRNA-Seq analysis. 87:1 - Sriram Boddeda, Marmar R. Moussa, Olajumoke B. Oladapo, Youla Ali, Nicholas Louque, Suryaveer Kapoor:
AtlasCollect: A Single Cell Data Atlas platform and Unified Platform for Datasets Collection and Integration. 88:1 - Nooshin KianvashRad, Dennis LaJeunesse, Lifeng Zhang:
The Effect of Electrospun Polyacrylonitrile on Antifungal Drug Sensitivity in Candida albicans. 89:1 - Yeawon Lee, Xiaoyang Wang, Christopher Yang:
Automated Clinical Problem Detection from SOAP Notes using a Collaborative Multi-Agent LLM Architecture. 90:1 - Zeyu Yao, Jake Y. Chen:
BioRSP: Angular Scanning for Directional Gene Expression Enrichment in Single-Cell Embeddings. 91:1 - Ouldouz Ghorbani, Ahmed Helmy, Qingrong Jackie Wu, Yaorong Ge:
Examining Radiation Therapy Planning Knowledge in Large Language Models. 92:1 - Sayed Mehedi Azim, Renuka Kumar, Brian Corbett, Iman Dehzangi:
MT-UGAN: Multi-task GANs for Automatic Segmentation and Identification of Hippocampal Regions. 93:1 - Zooey Lan:
A Novel AI Approach to Analyze the Cardiovascular Effects of Artificial Sweeteners Using Daphnia magna. 94:1 - Ellen A Huang, Xing Tan:
ATOMS: An Action Theory Of Moran System. 95:1 - Frank Tan, Isaac Huang, Jimmy Xiangji Huang:
Retrospective Inference of Evolutionary Parameters in the Moran Process Using ChatGPT. 96:1 - Logan Nicholas Day, Filip Jagodzinski, James Tessmer, Bogdan Trigubov, Emelia Galante:
Protein-Protein Interface Angle Change (∆FA) as a Descriptor of Mutation-Induced Structural Perturbations. 97:1 - Giuditta Benincasa, Claudio Napoli:
Network-Oriented Genome-Wide DNA Methylation Study of Circulating CD4+ T Lymphocytes of Patients with Heart Failure: DNA Methylation and Heart Failure. 98:1 - Giuditta Benincasa, Claudio Napoli:
Network Analysis of Methylomics in Patients with Brugada: DNA Methylation and Brugada Syndrome. 99:1 - Qiuyue Hu, Rui Zhou, Zhihao Wang, Liangzhen Zheng, Yanjie Wei:
Learning the native-like codons with a 5'UTR and RNA secondary structure aided species-informed transformer model. 100:1 - Lang Leo Xiong:
Evaluating the Impact of Human Segmentation on AI-Based Pancreatic Cancer Detection in CT Scans. 101:1 - Shiv Shankar:
Controllable Flow-based Hybrid Space Protein Generation. 102:1 - Shiv Shankar:
Using Diffusion Planner for Cell Fate Reprogramming. 103:1 - Saaketh Bhojanam, Sohum Mehta:
Cell-Type-Aware Single-Cell ML Reveals Distinct Biomarkers for Sarcoidosis Prognosis and CBD Differentiation. 104:1 - Saaketh Bhojanam, Sohum Mehta:
Privacy-Preserving Genomic Similarity Search via Enhanced Homomorphic Encryption with BLAST-Concordant Algorithms. 105:1 - Fnu Hridyanshu:
Thermodynamically Consistent Neural Models of Protein Folding Kinetics. 106:1
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